

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
  <meta charset="utf-8">
  
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  
  <title>openchem.utils.logger &mdash; OpenChem 0.1 documentation</title>
  

  
  
  
  

  

  
  
    

  

  <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
  <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
    <link rel="index" title="Index" href="../../../genindex.html" />
    <link rel="search" title="Search" href="../../../search.html" /> 

  
  <script src="../../../_static/js/modernizr.min.js"></script>

</head>

<body class="wy-body-for-nav">

   
  <div class="wy-grid-for-nav">

    
    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
      <div class="wy-side-scroll">
        <div class="wy-side-nav-search">
          

          
            <a href="../../../index.html">
          

          
            
            <img src="../../../_static/logo.png" class="logo" alt="Logo"/>
          
          </a>

          

          
<div role="search">
  <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
    <input type="text" name="q" placeholder="Search docs" />
    <input type="hidden" name="check_keywords" value="yes" />
    <input type="hidden" name="area" value="default" />
  </form>
</div>

          
        </div>

        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
          
            
            
              
            
            
              <ul>
<li class="toctree-l1"><a class="reference internal" href="../../../index.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../installation_instructions.html">Installation instructions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../installation_instructions.html#general-installation">General installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../installation_instructions.html#installation-with-docker">Installation with Docker</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../how_to_run_tutorial.html">How to define and train models</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../how_to_run_tutorial.html#arguments-for-launch-py">Arguments for launch.py</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../how_to_run_tutorial.html#arguments-for-run-py">Arguments for run.py</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../how_to_run_tutorial.html#configuration-file">Configuration file</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../how_to_run_tutorial.html#launching-jobs">Launching jobs</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../tutorials/blocks.html">Tutorials and Recipes</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../tutorials/gcnn_tutorial.html">GraphCNN for predicting logP</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/gcnn_tutorial.html#defining-node-attributes">Defining node attributes</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/gcnn_tutorial.html#loading-data">Loading data</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/gcnn_tutorial.html#defining-model-architechture">Defining model architechture</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/gcnn_tutorial.html#training-and-evaluating-the-model">Training and evaluating the model</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../tutorials/tox21_tutorial.html">Tox21 Challenge</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/tox21_tutorial.html#loading-data">Loading data</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/tox21_tutorial.html#defining-evaluation-function">Defining evaluation function</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/tox21_tutorial.html#defining-model-architechture">Defining model architechture</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../tutorials/tox21_tutorial.html#training-and-evaluating-the-model">Training and evaluating the model</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../api-docs/blocks.html">API documentation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/models.html">models</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/models.html#module-models.openchem_model">openchem_model</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/models.html#module-models.Smiles2Label">Smiles2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/models.html#module-models.Graph2Label">Graph2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/models.html#module-models.MoleculeProtein2Label">MoleculeProtein2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/models.html#vanilla-model">vanilla_model</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/modules.html">modules</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/modules.encoders.html">encoders</a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.encoders.html#module-modules.encoders.openchem_encoder">openchem_encoder</a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.encoders.html#module-modules.encoders.rnn_encoder">rnn_encoder</a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.encoders.html#cnn-encoder">cnn_encoder</a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.encoders.html#gcnn-encoder">gcnn_encoder</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/modules.embeddings.html">embeddings</a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.embeddings.html#module-modules.embeddings.openchem_embedding">openchem_embedding</a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.embeddings.html#module-modules.embeddings.basic_embedding">basic_embedding</a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../api-docs/modules.embeddings.html#positional-embedding">positional_embedding</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/modules.mlp.html">mlp</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/layers.html">layers</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/layers.html#module-layers.conv_bn_relu">conv_bn_relu</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/layers.html#module-layers.gcn">gcn</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/data.html">data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.smiles_data_layer">smiles_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.graph_data_layer">graph_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.smiles_protein_data_layer">smiles_protein_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.vanilla_data_layer">vanilla_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.smiles_enumerator">smiles_enumerator</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/data.html#module-data.utils">utils</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/criterion.html">criterion</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/criterion.html#module-openchem.criterion.multitask_loss">multitask_loss</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/optimizer.html">optimizer</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/optimizer.html#module-optimizer.openchem_optimizer">openchem_optimizer</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/optimizer.html#module-optimizer.openchem_lr_scheduler">openchem_lr_scheduler</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../api-docs/utils.html">utils</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/utils.html#module-openchem.utils.graph">graph</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/utils.html#id1">utils</a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../api-docs/utils.html#module-openchem.utils.logger">logger</a></li>
</ul>
</li>
</ul>
</li>
</ul>

            
          
        </div>
      </div>
    </nav>

    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">

      
      <nav class="wy-nav-top" aria-label="top navigation">
        
          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
          <a href="../../../index.html">OpenChem</a>
        
      </nav>


      <div class="wy-nav-content">
        
        <div class="rst-content">
        
          















<div role="navigation" aria-label="breadcrumbs navigation">

  <ul class="wy-breadcrumbs">
    
      <li><a href="../../../index.html">Docs</a> &raquo;</li>
        
          <li><a href="../../index.html">Module code</a> &raquo;</li>
        
      <li>openchem.utils.logger</li>
    
    
      <li class="wy-breadcrumbs-aside">
        
      </li>
    
  </ul>

  
  <hr/>
</div>
          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
           <div itemprop="articleBody">
            
  <h1>Source code for openchem.utils.logger</h1><div class="highlight"><pre>
<span></span><span class="c1"># Code referenced from</span>
<span class="c1"># https://gist.github.com/gyglim/1f8dfb1b5c82627ae3efcfbbadb9f514</span>
<span class="kn">import</span> <span class="nn">tensorflow</span> <span class="k">as</span> <span class="nn">tf</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">scipy.misc</span>

<span class="k">try</span><span class="p">:</span>
    <span class="kn">from</span> <span class="nn">StringIO</span> <span class="k">import</span> <span class="n">StringIO</span>  <span class="c1"># Python 2.7</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
    <span class="kn">from</span> <span class="nn">io</span> <span class="k">import</span> <span class="n">BytesIO</span>  <span class="c1"># Python 3.x</span>


<div class="viewcode-block" id="Logger"><a class="viewcode-back" href="../../../api-docs/utils.html#openchem.utils.logger.Logger">[docs]</a><span class="k">class</span> <span class="nc">Logger</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>

    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">log_dir</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;Create a summary writer logging to log_dir.&quot;&quot;&quot;</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">writer</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">summary</span><span class="o">.</span><span class="n">FileWriter</span><span class="p">(</span><span class="n">log_dir</span><span class="p">)</span>

<div class="viewcode-block" id="Logger.scalar_summary"><a class="viewcode-back" href="../../../api-docs/utils.html#openchem.utils.logger.Logger.scalar_summary">[docs]</a>    <span class="k">def</span> <span class="nf">scalar_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">step</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;Log a scalar variable.&quot;&quot;&quot;</span>
        <span class="n">summary</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="p">[</span><span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="n">tag</span><span class="o">=</span><span class="n">tag</span><span class="p">,</span>
                                                     <span class="n">simple_value</span><span class="o">=</span><span class="n">value</span><span class="p">)])</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">writer</span><span class="o">.</span><span class="n">add_summary</span><span class="p">(</span><span class="n">summary</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span></div>

<div class="viewcode-block" id="Logger.image_summary"><a class="viewcode-back" href="../../../api-docs/utils.html#openchem.utils.logger.Logger.image_summary">[docs]</a>    <span class="k">def</span> <span class="nf">image_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">images</span><span class="p">,</span> <span class="n">step</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;Log a list of images.&quot;&quot;&quot;</span>

        <span class="n">img_summaries</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">img</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">images</span><span class="p">):</span>
            <span class="c1"># Write the image to a string</span>
            <span class="k">try</span><span class="p">:</span>
                <span class="n">s</span> <span class="o">=</span> <span class="n">StringIO</span><span class="p">()</span>
            <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
                <span class="n">s</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
            <span class="n">scipy</span><span class="o">.</span><span class="n">misc</span><span class="o">.</span><span class="n">toimage</span><span class="p">(</span><span class="n">img</span><span class="p">)</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;png&quot;</span><span class="p">)</span>

            <span class="c1"># Create an Image object</span>
            <span class="n">img_sum</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="n">encoded_image_string</span><span class="o">=</span><span class="n">s</span><span class="o">.</span><span class="n">getvalue</span><span class="p">(),</span>
                                       <span class="n">height</span><span class="o">=</span><span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
                                       <span class="n">width</span><span class="o">=</span><span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
            <span class="c1"># Create a Summary value</span>
            <span class="n">img_summaries</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="n">tag</span><span class="o">=</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">/</span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">i</span><span class="p">),</span>
                                                  <span class="n">image</span><span class="o">=</span><span class="n">img_sum</span><span class="p">))</span>

        <span class="c1"># Create and write Summary</span>
        <span class="n">summary</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="n">img_summaries</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">writer</span><span class="o">.</span><span class="n">add_summary</span><span class="p">(</span><span class="n">summary</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span></div>

<div class="viewcode-block" id="Logger.histo_summary"><a class="viewcode-back" href="../../../api-docs/utils.html#openchem.utils.logger.Logger.histo_summary">[docs]</a>    <span class="k">def</span> <span class="nf">histo_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">values</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;Log a histogram of the tensor of values.&quot;&quot;&quot;</span>

        <span class="c1"># Create a histogram using numpy</span>
        <span class="n">counts</span><span class="p">,</span> <span class="n">bin_edges</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">values</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="n">bins</span><span class="p">)</span>

        <span class="c1"># Fill the fields of the histogram proto</span>
        <span class="n">hist</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">HistogramProto</span><span class="p">()</span>
        <span class="n">hist</span><span class="o">.</span><span class="n">min</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
        <span class="n">hist</span><span class="o">.</span><span class="n">max</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
        <span class="n">hist</span><span class="o">.</span><span class="n">num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">prod</span><span class="p">(</span><span class="n">values</span><span class="o">.</span><span class="n">shape</span><span class="p">))</span>
        <span class="n">hist</span><span class="o">.</span><span class="n">sum</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
        <span class="n">hist</span><span class="o">.</span><span class="n">sum_squares</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">values</span> <span class="o">**</span> <span class="mi">2</span><span class="p">))</span>

        <span class="c1"># Drop the start of the first bin</span>
        <span class="n">bin_edges</span> <span class="o">=</span> <span class="n">bin_edges</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>

        <span class="c1"># Add bin edges and counts</span>
        <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">bin_edges</span><span class="p">:</span>
            <span class="n">hist</span><span class="o">.</span><span class="n">bucket_limit</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">edge</span><span class="p">)</span>
        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">counts</span><span class="p">:</span>
            <span class="n">hist</span><span class="o">.</span><span class="n">bucket</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>

        <span class="c1"># Create and write Summary</span>
        <span class="n">summary</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="p">[</span><span class="n">tf</span><span class="o">.</span><span class="n">Summary</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="n">tag</span><span class="o">=</span><span class="n">tag</span><span class="p">,</span> <span class="n">histo</span><span class="o">=</span><span class="n">hist</span><span class="p">)])</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">writer</span><span class="o">.</span><span class="n">add_summary</span><span class="p">(</span><span class="n">summary</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">writer</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span></div></div>
</pre></div>

           </div>
           
          </div>
          <footer>
  

  <hr/>

  <div role="contentinfo">
    <p>
        &copy; Copyright 2018, Mariya Popova.

    </p>
  </div>
  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 

</footer>

        </div>
      </div>

    </section>

  </div>
  


  

    <script type="text/javascript">
        var DOCUMENTATION_OPTIONS = {
            URL_ROOT:'../../../',
            VERSION:'0.1',
            LANGUAGE:'None',
            COLLAPSE_INDEX:false,
            FILE_SUFFIX:'.html',
            HAS_SOURCE:  true,
            SOURCELINK_SUFFIX: '.txt'
        };
    </script>
      <script type="text/javascript" src="../../../_static/jquery.js"></script>
      <script type="text/javascript" src="../../../_static/underscore.js"></script>
      <script type="text/javascript" src="../../../_static/doctools.js"></script>
      <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>

  

  <script type="text/javascript" src="../../../_static/js/theme.js"></script>

  <script type="text/javascript">
      jQuery(function () {
          SphinxRtdTheme.Navigation.enable(true);
      });
  </script>  

  <style>
    /* Sidebar header (and topbar for mobile) */
    .wy-side-nav-search, .wy-nav-top {
      background: #99badd;
    }
  </style>


</body>
</html>